title: SINGLE-CELL CHARACTERIZATION OF A MODEL OF POLY I:C-STIMULATED PERIPHERAL BLOOD MONONUCLEAR CELLS IN SEVERE ASTHMA

status: Public on Apr 22 2021

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

summary: Background: Asthma has been associated with impaired interferon response. Multiple cell types have been implicated in such response impairment and may be responsible for asthma immunopathology. However, existing models to study the immune response in asthma are limited by bulk profiling of cells. Our objective was to Characterize a model of peripheral blood mononuclear cells (PBMCs) of patients with severe asthma (SA) and its response to the TLR3 agonist Poly I:C using two single-cell methods.   Methods: Two complementary single-cell methods, DropSeq for single-cell RNA sequencing (scRNA-Seq) and mass cytometry (CyTOF), were used to profile PBMCs of SA patients and healthy controls (HC). Poly I:C-stimulated and unstimulated cells were analyzed in this study.   Results: PBMCs (n=9,414) from five SA (n=6,099) and three HC (n=3,315) were profiled using scRNA-Seq. Six main cell subsets, namely CD4+ T cells, CD8+ T cells, natural killer (NK) cells, B cells, dendritic cells (DCs), and monocytes, were identified. CD4+ T cells were the main cell type in SA and demonstrated a pro-inflammatory profile characterized by increased JAK1 expression. Following Poly I:C stimulation, PBMCs from SA had a robust induction of interferon pathways compared with HC. CyTOF profiling of Poly I:C stimulated and unstimulated PBMCs (n=160,000) from the same individuals (SA=5; HC=3) demonstrated higher CD8+ and CD8+ effector T cells in SA at baseline, followed by a decrease of CD8+ effector T cells after poly I:C stimulation.  Conclusions: Single-cell profiling of an in vitro model using PBMCs in patients with SA identified activation of pro-inflammatory pathways at baseline and strong response to Poly I:C, as well as quantitative changes in CD8+ effector cells. Thus, transcriptomic and cell quantitative changes are associated with immune cell heterogeneity in this model to evaluate interferon responses in severe asthma.

overall_design: PBMCs from five patients with severe asthma and three healthy controls were compared at baseline and following poly (I:C) stimulation.


title: RNA-seq analysis of the gene expression profile regulated by CHIR and Spautin-1 in mouse ESCs

status: Public on Apr 21 2021

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

type: Expression profiling by high throughput sequencing

summary: Purpose:The goals of this study is to analyze the gene expession pattern in mouse embryonic stem cells (ESCs) treated with CHIR99021(CHIR) in the presence or absence of Spautin-1 for 24 h.

overall_design: 46C mouse ESCs cultured in serum-containing medium supplemented with 3 µM CHIR or 3 µM CHIR plus 8 µM Spautin-1 (CHIR_SP) for 24 h were collected by using Trizol. These samples were sent to BGI (Shenzhen, China) company to do deep sequencing by using MGI2000.

first: Shoudong

last: Ye


title: Parallel functional testing identifies enhancers active in early postnatal mouse brain

status: Public on Apr 15 2021

city: Davis

first: Alexander

middle: Star

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

country: USA

institute: University of California Davis

summary: Cis-regulatory elements such as enhancers play critical regulatory roles in modulating developmental transcription programs and driving cell-type specific and context-dependent gene expression in the brain. The development of massively parallel reporter assays has enabled high-throughput functional screening of candidate DNA sequences for enhancer activity. Tissue-specific screening of in vivo enhancer function at scale has the potential to greatly expand our understanding of the role of non-coding sequences in development, evolution, and disease. Here, we adapted the self-transcribing regulatory element MPRA strategy for delivery to early postnatal mouse brain via recombinant adeno-associated virus (rAAV). We identify putative enhancers capable of driving reporter gene expression in mouse forebrain, including regulatory elements within an intronic CACNA1C linkage disequilibrium block associated with risk in neuropsychiatric disorder genetic studies. Paired screening and single enhancer in vivo functional testing, as we show here, represents a powerful approach towards characterizing regulatory activity of enhancers and understanding how enhancer sequences organize gene expression in normal and pathogenic brain development.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: 1) Massively Parallel Reporter Assays (MPRA) testing 408 ~900 bp human amplicons in AAV vector: 4 paired RNA and DNA replicates, 1 AAV plasmid library; 1 high-PCR-cycle technical replicate. Illumina PE150 reads. 2) Massively Parallel Reporter Assay with 16 ~900 bp mouse amplicons with human orthologs (mini_MPRA): 4 RNA replicates and 1 AAV plasmid library. Illumina PE75 reads.

first: Jason

middle: T

last: Lambert

first: Linda

last: Su-Feher

first: Karol

last: Cichewicz

first: Tracy

middle: L

last: Warren

first: Iva

last: Zdilar

first: Yurong

last: Wang

first: Kenneth

middle: J

last: Lim

first: Jessica

last: Haigh

first: Sarah

last: Morse

first: Cesar

middle: P

last: Canales

first: Tyler

middle: W

last: Stradleigh

first: Erika

last: Castillo

first: Viktoria

last: Haghani

first: Spencer

last: Moss

first: Hannah

last: Parolini

first: Diana

last: Quintero

first: Diwash

last: Shrestha

first: Daniel

last: Vogt

first: Leah

middle: C

last: Byrne

first: Alex

middle: S


title: Architectural role of cell-fate-instructive transcription factor MyoD in orchestrating 3D genome organization in muscle cells.

status: Public on May 01 2021

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cell-type specific transcription factors play important roles in lineage specification whereas it is largely unknown whether and how they regulate context-specific 3D chromatin structure. Herein, we comprehensively mapped 3D chromatin organization in muscle cells and uncovered master transcription factor MyoD-mediated myogenic lineage specific chromatin structures in comparison with embryonic stem cells and neuronal cells. We discovered that MyoD is significantly enriched at loop anchor and mediate numerous chromatin loops without CTCF binding. Importantly, we found MyoD-involved interactions were dramatically disrupted when MyoD was absent, implying MyoD is an indispensable factor for loop regulation. Additionally, MyoD mediated shorter, weaker and more dynamic interactions, especially enhancer - enhancer and enhancer - promoter loops. Finally, MyoD mainly regulate cell type-specific contacts which were concomitant to muscle cell specific gene expression. Collectively, we utilized high resolution Hi-C data and genetic model to prove a master transcriptional factor govern lineage specific chromatin loops. We propose that MyoD-mediated interactions are a general feature of lineage specific transcriptional factors-regulated gene expression.

overall_design:
Hi-C, ChIP-seq and RNA-seq of wildtype and MyoD-KO  mouse during skeletal muscle differentiation
Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (under accession CRA002490,https://bigd.big.ac.cn/gsa/browse/CRA002490).

first: Fengling

last: Chen

first: Qian


title: Transcriptional response of Mycobacterium tuberculosis to cigarette smoke condensate

city: Cape Town

first: Danicke

last: Willemse

state: Western Cape

address: Main Rd, Observatory, Cape Town, 7925

department: Medicine

country: South Africa

institute: University of Cape Town

summary: Mycbacterium tuberculosis was exposed to cigarette smoke condensate (CSC) in 7H9 dextrose culture media. The transcriptional response to cigarette smoke condensate was compared to that of exposure to the CSC diluent, DMSO..

overall_design: RNA was extracted from Mycobacterium tuberculosis after 3 and 24h of exposure to CSC or its diluent, DMSO,  in 7H9 dextrose and RNA-seq done.

first: D

first: C

last: Moodley

first: S

last: Mishra

last: Kaushal


title: Gene expression profiling data following PTBP1 knockout in MKN-28 cells

status: Public on Apr 14 2021

city: Guangzhou

first: Min

last: Deng

address: 78 Hengzhigang Road

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

summary: We analysed the transcriptome profile by RNA-seq in PTBP1 knockout and control MKN-28 cells.

overall_design: Compare the mRNA profiles between PTBP1 knockout and the control MKN-28 cells.


title: Comparative multi-tissue profiling reveals extensive tissue-specificity in transcriptome reprogramming upon cold exposure

city: Genève

first: Noushin

last: Hadadi

address: 1 rue Michel-Servet

department: Physiology and Cellular Metabolism

country: Switzerland

institute: University of Geneva

summary: comparative multi-tissue RNA sequencing using a panel of organs including spleen, bone marrow, spinal cord, brain, hypothalamus, ileum, liver, subcutaneous-, visceral- and brown adipose tissues

overall_design: mRNA profiles of ten tissues of WT male 8 weeks old C57BL/6J mice

first: Martina

last: Spiljar


title: Enhancer architecture-dependent multilayered transcriptional regulation orchestrates RA signal-induced early differentiation of ESC

status: Public on Apr 16 2021

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

summary: Signaling pathway driven target gene transcriptions are critical for fate determination of embryonic stem cells (ESC), but enhancer architecture-dependent transcriptional regulation remains largely unclear in this process. Here, we described a complex enhancer architecture-dependent multilayered transcriptional regulation that orchestrates retinoic acid (RA) signal-induced early differentiation of ESC. Specifically, we identified Hoxa1 and lncRNA Halr1 as the direct downstream target genes of RA signal. Chromosome conformation capture based screens show that increased enhancer interactions promoted by RA signal are essential for Hoxa1 and Halr1 expressions during early ESC differentiation. Furthermore, we find that HOXA1 promotes Halr1 expression through direct binding to enhancers; conversely, absence of Halr1 RNA enhances interaction between Hoxa1 chromatin and multiple enhancers, but weakens interaction with HoxA cluster internal chromatin, thereby promoting RA signal-induced Hoxa1 overactivation and early differentiation of ESC. These results indicate that Halr1 binds to chromatin not only acts as a brake to orchestrate interaction between enhancers and Hoxa1 chromatin, but also acts as a binder to maintain chromatin interaction within HoxA cluster. In summary, these findings reveal a complex multilayered transcriptional regulation involving the synergistic regulation of enhancer, transcription factor and lncRNA, and that increases our understanding of the intrinsic molecular mechanisms of RA signal-induced ESC differentiation.

overall_design: At least 2 biological replicates were analyzed for each experimental condition. WT and knockout cells were RNA-seq after RA treatment for 24h or untreatment. Enhancer or Hoxa1 Capture-C were done in WT and Halr1-KO cells, in triplicate, under RA induction or untreatmnet for 24 h.

first: Wange

last: Lu

first: Guangsong

last: Su

first: Wenbin

last: Wang


title: Transcriptome analysis of SREBF1 silencing and overexpression in thyroid cancer cells

status: Public on Apr 13 2021

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: Malignant thyroid tumors have altered lipid metabolism. Sterol regulatory element-binding transcription factor 1 (SREBF1), also known as sterol regulatory element-binding protein 1 (SREBP-1), regulates cellular lipid homeostasis. We found that SREBF1 expression is a prognostic factor in patients with thyroid cancer and planned to elucidate its oncogenic mechanisms.

overall_design: Human thyroid cancer cells BHT-101 and FTC-133 were transfected with SREBF1-specific siRNA or a control siRNA, and 8505C and K1 cells were transfected with the SREBF1-overexpressing vector or an empty vector. Cellular RNA was submitted to RNA sequencing.


title: RIP-seq analysis of PTBP1-bound RNAs

type: Non-coding RNA profiling by high throughput sequencing

summary: To reveal PTBP1-bound RNAs, we conducted RNA immunoprecipitation sequencing (RIP-seq) with total RNA samples from MKN-28 cells.

overall_design: MKN-28 cells were used for RIP-seq. Fold enrichment of RNAs pulled down by PTBP1 antibody was detected by High-throughput Sequencing, and IgG served as a negative control.


title: LncRNA expression profile in gastric cancer specimens and adjacent noncancerous tissues

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We implemented lncRNA microarray analysis in 5 paired gastric cancer tissues and adjacent noncancerous tissues to identify differential expression of lncRNAs and mRNAs in gastric cancer.

overall_design: The global expression profile of lncRNA and mRNA was detected with total RNA from 5 paired gastric cancer and adjacent noncancerous tissues using LncRNA + mRNA Human Gene Expression Microarray V4.0. The RNA from gastric cancer tissue were labeled with Cy5 dye and those of adjacent tissues were labeled with Cy3 dye as a reference.

first: Donglan

last: Huang


title: Targeted amplicon sequencing data from specified genomic amplicons

status: Public on Apr 10 2021

first: Hao

last: Wu

address: HaiDian, Beijing

department: Peking University

institute: Peking University

summary:
Purpose: The goals of this study are to introduce a new genome editing tool, which has the higher editing scope than the original genome editing tools.
Methods: First, we transfected PE2 (the original prime editing tool, prime editor2), PE3 (the original prime editing tool, prime editor3) and HOPE (the new tool we developed in this study) vectors into human cells, respectively. Then, we harvested the genomic DNA form the transfected cells and amplified the specified amplicons. Finally, we used targeted amplicon sequencing approach to compare the editing efficiency and presion of the new tool with the original reported tools.
Results: Our new genome editing tool improves the editing efficiency of prime editing without increasing the risk of undesired indels formation.
Conclusions: We deleveped a new genome editing tool to increase the likelihood of successful gene engineering.

overall_design: The targeted amplicon sequencing data were used to examine the editing efficiency and precision of the new tool in HEK293T or HCT116 cells.


title: Single-cell immunophenotyping of the fetal immune response to maternal SARS-CoV-2 infection

status: Public on Apr 06 2021

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: During the COVID-19 pandemic, thousands of pregnant women have been infected with SARS-CoV-2 worldwide. The short- and long-term implications of maternal SARS-CoV-2 infection on fetal and childhood well-being are unknown. To characterize the fetal immune response to maternal SARS-CoV-2 infection, we performed single-cell RNA sequencing and T cell receptor sequencing on cord blood mononuclear cells from infants born to mothers infected with SARS-CoV-2 in the third trimester. We identified widespread gene expression changes in cord blood leukocytes, including upregulation of interferon-stimulated genes (ISG) and of HLA genes in CD14+ monocytes; decreased activation of CD16+ monocytes; activation of plasmacytoid dendritic cells; and activation and exhaustion of NK cells and T CD8+ cells in the cord blood of infants born to SARS-CoV-2+ mothers.  Lastly, we observed fetal TCR repertoire clonal expansion in cord blood T cells from pregnancies complicated by maternal SARS-CoV-2 infection. Our results suggest that even in the absence of vertical transmission, SARS-CoV-2 maternal infection in the third trimester modulates the fetal immune system.

overall_design: Single-cell RNA-seq of cord blood mononuclearcells from COVID-positive and COVID-negative pregnancies, as well as T-cell receptor repertoire sequencing from the same samples


title: Convergent transcriptional responses to acquisition and amelioration of different conjugative plasmids

status: Public on Apr 17 2021

city: Liverpool

first: James

last: Hall

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: Aim: to identify the transcriptional responses to acquisition of conjugative megaplasmids by Pseudomonas fluorescens, and how these effects are impacted by known compensatory mutations. Full abstract TBC.

overall_design:
Examination of effects of megaplasmid acqusition, compensatory mutations, and their combination. Ten treatments in triplicate (30 samples overall). The overall design is broadly factorial, but for some treatments design was nested. Treatments include a no-plasmid baseline control, megaplasmids alone, compensatory mutations alone (where available), and all combinations (where available).

Definitions:
dPFLU4242 is a deletion of the gene PFLU4242 (∆PFLU4242)
PQBR57_0059_V100A is a single basepair mutation in the plasmid pQBR57 causing a V100A mutation in PQBR57_0059 (T299>C)
dgacS is a deletion of the gene gacS (PFLU3777, ∆gacS)
pQBR57 is a mercury resistance plasmid (see Hall et al. 2015 doi: 10.1111/1462-2920.12901)
pQBR103 is a mercury resistance plasmid


title: Quantifying full-length circular RNAs in cancer

city: Hong Kong

first: Hung On Ken

last: Yu

address: Department of Anatomical and Cellular Pathology, Faculty of Medicine

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Circular RNAs (circRNAs) have been found abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels using RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discovered circRNA isoforms differentially expressed between the two groups. Compared to the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain fewer microRNA response elements, demonstrating the importance of quantifying full-length circRNA isoforms.

overall_design: Four immortalized normal nasopharyngeal epithelial cell lines (NP69, NP361, NP460 and NPC550), 2 EBV-positive NPC cell lines (C666-1 and NPC43), 7 patient-derived xenografts (Xeno-666, Xeno-2117, Xeno-1915, Xeno-99186, C15, C17 and Xeno-32) and 2 patient tumor specimens (NPC-M1 and NPC-M2) were used in this study.

first: Ken

middle: H

first: Christina

last: Shi

first: Bo

first: Savio

last: Chow

first: Grace

last: Chung

first: Ke-En

last: Tan

first: Yat-Yuen

last: Lim

first: Anna

last: Tsang

first: Kwok-Wai

last: Lo

first: Kevin

middle: Y

last: Yip


title: Identification and Functional Analysis of MYEOV, KCNN4, S100A16 and DDX60L in Pancreatic Ductal Adenocarcinoma

city: Kunming

first: Hongjin

state: China / Yunnan

address: Xichang Road#295

institute: The NHC Key Laboratory of Drug Addiction Medicine

summary: siRNA of MYEOV, KCNN4, S100A16 and DDX60L treated MiaPaCa2 and PANC-1 cells were used for RNA-seq to identify the transcriptomic alterations.

overall_design: Examination of  knockdown MYEOV, KCNN4, S100A16 and DDX60L in MiaPaCa2 and PANC-1 cells.

first: Juehua


title: Identification of the OsbR regulon in Chromobacterium violaceum

status: Public on Apr 11 2021

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

country: Brazil

institute: Universidade de Sao Paulo

summary: Here, we described a novel transcriptional regulator belonging to the MarR family that we named OsbR (oxidative stress response and biofilm formation regulator) in the opportunistic pathogen Chromobacterium violaceum. Transcriptome profiling by DNA microarray using strains with deletion or overexpression of osbR showed that OsbR exert a global regulatory role in C. violaceum, regulating genes involved in oxidative stress response, nitrate reduction, biofilm formation, and several metabolic pathways. EMSA assays showed that OsbR binds to the promoter regions of several OsbR-regulated genes and the in vitro DNA binding activity was inhibited by oxidants. We demonstrated that the overexpression of osbR caused activation of ohrA even in the presence of the repressor OhrR, which resulted in improved growth under organic hydroperoxide treatment. We showed that the proper regulation of the nar genes by OsbR ensures an optimal growth of C. violaceum under anaerobic conditions by tuning the reduction of nitrate to nitrite. Finally, the osbR overexpressing strain showed reduction in biofilm formation and this phenotype correlated with the OsbR-mediated repression of two gene clusters encoding putative adhesins.

overall_design: Two experimental procedures comparing WT control vs. osbR mutant or WT overexpressing osbR vs. osbR mutant. Comparison was performed using three biological replicates.

first: Julia

middle: A

last: Alves

first: Maristela

last: Previato-Mello

first: Kelly

last: Barroso

first: José

middle: F


title: Genome-wide mapping of G-quadruplex structures with CUT&Tag

status: Public on Apr 27 2021

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (mESC), discovering G4 formation at active and poised promoters and enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mESCs. Further performing R-loop CUT&Tag, we demonstrate the widespread co-occurence of single-stranded DNA, G4s and R loops, suggesting an intricate interrelation of non-canonical DNA structures, transcription and the formation and turnover of G4s.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&Tag using G4-specific antibody, clone BG4, in human and mouse cell lines. CUT&Tag using R loop-specific antibody, clone S9.6, in human and mouse cell lines.

first: Jing

last: Lyu


title: miRNA regulatory landscape of EMT [mRNA-seq]

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: To investigate the transcriptional remodelling during EMT, we transfected normal murine mammary gland epithelial cells during a 4d TGFbeta treatment individually with siRNA against 46 transcription (co)factors or with 13 mature miRNA, all factors that blocked EMT in a phenotypic microscopy-based EMT screen upon RNAi . As a control, cells were transfected with siRNA/miRNA control followed by 4d TGFbeta treatment (mesenchymal control) or were left untreated (epithelial control). miRNA-sequencing  together with mRNA-sequencing of these EMT perturbations in combination with transcription factor binding and miRNA target prediction enabled us to build an interaction map between these EMT factors.

overall_design:
mRNA sequencing of NMuMG/E9 cells transfected with siRNA against 49 transcription (co)factors or with 13 mature miRNAs in replicates followed by treatment with TGFbeta for 4 days. Transfection was repeated and TGFbeta medium exchanged every three days. As an epithelial control, cells were transfected with siRNA or miRNA control constructs in the absence of TGFbeta while the mesenchymal control was treated for 4 days with TGFbeta after transfection of the control siRNA/miRNA constructs.

This series includes samples re-used from GSE86024. There are links on the foot of the records to the alternative sample.

first: Maren

last: Diepenbruck

first: Nathalie

last: Meyer-Schaller

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Transcription (co)factor regulatory landscape of EMT [mRNA-seq]

overall_design:
mRNA sequencing of NMuMG/E9 cells transfected with siRNA against 49 transcription (co)factors or with 13 mature miRNAs in replicates followed by treatment with TGFbeta for 4 days. Transfection was repeated and TGFbeta medium exchanged every three days. As an epithelial control, cells were transfected with siRNA or miRNA control constructs in the absence of TGFbeta while the mesenchymal control was treated for 4 days with TGFbeta after transfection of the control siRNA/miRNA constructs.

This series includes re-used samples from GSE112796. There are links on the foot of the records to the alternative sample.


title: Transcriptomic analysis of loss of Gli1 in neural stem cells responding to demyelination in the mouse brain.

status: Public on Mar 31 2021

city: New York

first: James

last: Salzer

state: NY

address: 435 East 30th street

department: Neuroscience

institute: New York University

summary: In the adult mammalian brain, Gli1 expressing neural stem cells reside in the subventricular zone and their progeny are recruited to sites of demyelination in the white matter where they regenerate oligodendrocytes, the myelin forming cells. Remarkably, genetic and pharmacologic inhibition of Gli1 enhances remyelination in the adult brain. To understand the molecular mechanisms involved, we performed a transcriptomic analysis to compare the expression of genes in Gli1 neural stem cells with either intact Gli1 expression or genetic loss of Gli1 from adult mice on control diet or cuprizone diet, which induces demyelination. These data will be a valuable resource for identifying therapeutic targets for enhancing remyelination in demyelinating diseases like multiple sclerosis.

overall_design:
Differential gene expression in fac-sorted fate-mapped Gli1 neural stem cells from the adult subventricular zone of Gli1-Het (Gli1 CreER/wt; Rgfp) and Gli1-null (Gli1 CreER/CreER; Rgfp) mice on control diet vs  0.2% cuprizone diet for 3 weeks. Total 12 samples were analyzed consisting of 3 replicates each from Gli1-Het mice on control diet, Gli1-Het mice on cuprizone diet, Gli1-Null mice on control diet and Gli1-Null mice on cuprizone diet.

Grant ID: DOH01-STEM5-2016-00305
Funding source: New York State DOH
Grant title: Mobilizing Neural Stem Cells for Remyelination
Name: James Salzer

first: Jayshree

last: Samanta


title: Transcription (co)factor and miRNA regulatory landscape of EMT (miRNA-seq)

overall_design: miRNA sequencing of NMuMG/E9 cells transfected with siRNA against 49 transcription (co)factors or with 13 mature miRNAs in replicates followed by treatment with TGFbeta for 4 days. Transfection was repeated and TGFbeta medium exchanged every three days. As an epithelial control, cells were transfected with siRNA or miRNA control constructs in the absence of TGFbeta while the mesenchymal control was treated for 4 days with TGFbeta after transfection of the control siRNA/miRNA constructs.


title: Genome wide sequencing analysis of primary cardiomyocytes treated with all-trans retinoic acid

status: Public on Apr 01 2021

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

summary: The retinoic acid (RA) signaling pathway is essential for cardiac development; however, cardiomyocytes, the main cell type of the heart, are considered to be unresposive to RA signaling. The goal of this study was to examine the effects of all-trans RA (atRA) treatment on cardiomyocytes isolated from E18.5 mouse embryos. We found that cardiomyocytes, contrary to previous findings, are indeed repsonsive to RA signaling and that many genes involved in cardiac developmental and repair processes were significantly deregulated upon atRA trearment. These findings have important implications for the heart development and regeneration fields.

overall_design: Transcriptional profiles of primary murine E18.5 cardiomyocytes treated with atRA or DMSO for 48 hours. Four biological replicates per treatment.

first: Fabio

last: Da Silva


title: Epigenomic Tensor Predicts Disease Subtypes and Reveals Constrained Tumor Evolution [RNA-Seq II]

status: Public on Mar 30 2021

city: Urbana

first: Jun

last: Song

state: IL

address: 1110 West Green Street, MC 704

department: Department of Physics

institute: University of Illinois, Urbana-Champaign

summary: Understanding the epigenomic evolution and specificity of disease subtypes from complex patient data remains a major biomedical problem. We here present DeCET (Decomposition and Classification of Epigenomic Tensors), an integrative computational approach for simultaneously analyzing hierarchical heterogeneous data, to identify robust epigenomic differences between tissue types, differentiation states, and disease subtypes. Applying DeCET to our own data from 21 uterine benign tumor (leiomyoma) patients identifies distinct epigenomic features discriminating normal myometrium and leiomyoma subtypes. Leiomyomas possess preponderant alterations in distal enhancers and long-range histone modifications confined to chromatin contact domains that constrain the evolution of pathological epigenomes. Moreover, we demonstrate the power and advantage of DeCET on multiple publicly available epigenomic datasets representing different cancers and cellular states. Epigenomic features extracted by DeCET can thus help improve our understanding of disease states, cellular development, and differentiation, thereby facilitating future therapeutic, diagnostic and prognostic strategies.

overall_design: Primary myometrial cells were obtained from three patients and treated with empty or V5-tagged HOXA13 vector using lentiviral transduction. RNA was harvested from these cells and used for next generation sequencing. Basecalls were performed using RTA v.2.4.11 on Nextseq instrument. Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired. After adapter trimming reads were aligned to the hg19 genome with the UCSC knownGene annotation with STAR options --quantmode. The fourth column of the quantmode output was extracted to obtain reads aligning to features in the correct orientation.

first: Jacob

middle: R

last: Leistico

first: Priyanka

last: Saini

first: Christopher

last: Futtner

first: Miroslav

last: Hejna

first: Yasuhiro

last: Omura

first: Pritin

middle: N

last: Soni

first: Poorva

last: Sandlesh

first: Magdy

last: Milad

first: Jian-Jun

last: Wei

first: Serdar

last: Bulun

middle: B

last: Parker

first: Grant

middle: D

last: Barish

first: Debabrata

last: Chakravarti


title: Epigenomic Tensor Predicts Disease Subtypes and Reveals Constrained Tumor Evolution [ATAC-seq]

overall_design: ATAC-seq was used to assess chromatin accessibility in matched leiomyoma and healthy myometrium tissue samples from 8 patients. Basecalls were performed using RTA v.2.4.11 on Nextseq instrument. Sequenced reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired. Trimmed reads were aligned to the hg19 genome using bowtie2 v2.3.2 with parameters --end-to-end --sensitive --score-min L,-1.5,-0.3 --no-unal. Aligned reads were filtered using samtools v1.7 view with parameters -b -f 2 -F 2828 -F 1024 -q13. Peaks were called from the filtered alignment files using MACS2 v2.1.1 with parameters -f BAMPE -g hs -B --keep-dup 1.

first: James


title: Epigenomic Tensor Predicts Disease Subtypes and Reveals Constrained Tumor Evolution [RNA-seq_HOXA13 KD]

overall_design: Primary leiomyoma cells were obtained from two patients and treated with HOXA13 and/or control shRNA, RNA was isolated from these cells and next generation sequencing was performed. Basecalls were performed using RTA v.2.4.11 on Nextseq instrument. Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired. After adapter trimming reads were aligned to the hg19 genome with the UCSC knownGene annotation with STAR options --quantmode. The fourth column of the quantmode output was extracted to obtain reads aligning to features in the correct orientation.


title: Epigenomic Tensor Predicts Disease Subtypes and Reveals Constrained Tumor Evolution [RNA-seq]

overall_design: RNA was isolated from fresh-frozen tissues comprising uterine leiomyomas and matched myometrium from 20 patients. Basecalls were performed using RTA v.2.4.11 on Nextseq instrument. Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired. After adapter trimming reads were aligned to the hg19 genome with the UCSC knownGene annotation with STAR options --quantmode. The fourth column of the quantmode output was extracted to obtain reads aligning to features in the correct orientation. The principal components are obtained using DESeq2 plotPCA modified to return the first 10 PCs. Prior to PCA, a regularized log transform is applied to the count data (DESeq2 rlog option blind=False).


title: The Cryptococcal Central Nervous System Transcriptome during Human Disease

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

summary: The transcriptional responses of cryptococcus during human infection are dynamic and highly dependent on the immediate signals from the environment.  We examined the RNA-Seq profiles of Cryptococcus isoalted from human CSF and in comparison with to the same isolate's response to the stresses of artificial CSF and within the rabbit subarachnoid space as well as growth in nutritious media with little or no stress. By comparing these transcriptomes, we have identified regulated genes and categorized them by networks and functional classifications to identify candidate genes essential for yeast survival and as well as those uniformly expressed in CSF across diverse isolates that may be markers for the human disease state.

overall_design: The cryptococcal transcriptomes directly from 30 yeast isolates from human CNS and within four different conditions. In total, there are 30 human CSF,  10 rabbit CSF (rCSF), 10 artificial CSF, 29 capsule-inducing media (CAP), and 29 rich media (YPD). The rabbit CSF samples are collected from two time points, 1-day and 4-day. This sampe set include three lineages, VNI, VNBI, and VNBII.

first: Chen-Hsin

last: Yu

first: Jennifer

last: Tenor

first: Poppy

last: Sephton-Clark

first: Christina

last: Cuomo


title: The study of alternative splicing events in human induced pluripotent stem cells from a Down's syndrome patient

status: Public on Mar 28 2021

city: shanghai

first: Yunjie

last: Wang

address: West Beijing Road 1400

institute: Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University

summary: We employed the GeneChip Human Transcriptome Array 2.0 (HTA 2.0) for the global gene analysis with hiPSCs from DS and healthy individuals. Examining differentially expressed genes (DEGs) in these groups and focusing on specific transcripts with Alternative Splicing.

overall_design: Total RNA of hiPSCs from DS and healthy individuals was  extracted and amplified 100 ng of RNA per sample were then hybridized on GeneChip Human Transcriptome Array 2.0 (HTA 2.0) (Affymetrix, Thermofischer scientific).  Differentially expressed genes (DEGs) and alternative splicing events in these groups were examined.

first: Zexu

last: Li

first: Guangheng

last: Yang

first: Linlin

last: Cai

first: Fan

first: Yaqiong

last: Zhang

first: Qingwen

last: Ma

first: Fanyi

last: Zeng


title: Identification and Functional Analysis of Novel Oncogenes in Pancreatic Ductal Adenocarcinoma

first: Hongjin

last: Wu

summary: For identifying the specific expressed genes in PDAC, we constructed sequencing libraries from polyadenylated-RNA extracted from 6 PDAC specimens and 6 non-tumor adjacent tissues.

overall_design: Examination of genes expression in PDAC and adjacent tissues.

first: Juehua


title: Epigenomic Tensor Predicts Disease Subtypes and Reveals Constrained Tumor Evolution

first: Jun

last: Song

overall_design: Examination of histone modifications H3K27ac, H3K4me3, and H3K4me1 with controls in fresh-frozen tissues from 27 uterine leiomyoma samples from 25 patients, and matched healthy myometrium for 21 of these patients. Basecalls were performed using RTA v.2.4.11 on Nextseq instrument. Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13. After adapter trimming reads were aligned to the hg19 genome using Bowtie2 v2.3.2 with parameters --end-to-end --sensitive --score-min L,-1.5,-0.3 --no-unal. Aligned reads were filtered for PCR duplicates using Picard v2.10.1 and then further filtered using samtools v1.7 with parameters -b -F 3588 -q 13. The filtered reads were sorted and converted to bed format. Lastly reads overlapping repeat regions identified by RepeatMaser or segmental duplication regions identified by Variant Tools were removed using bedtools v2.26.0 subtract -A. The code for generating the processed files from the filtered bed files can be found at https://github.com/jssong-lab/DeCET. Peak calling for histone modification ChIP-seq was performed relative to a corresponding control using MACS2 (options –broad -g hs –broad-cutoff 0.05) after removing reads overlapping repeat regions.

first: Jacob

last: Leistico

first: Priyanka

last: Saini

first: Christopher

last: Futtner

first: Miroslav

last: Hejna

first: Yasuhiro

last: Omura

first: Pritin

last: Soni

first: Poorva

last: Sandlesh

first: Magdy

last: Milad

first: Jian-Jun

last: Wei

first: Serdar

last: Bulun

first: Grant

first: Debabrata


title: Key role of dysregulated SF3A3 translation in MYC-induced breast tumorigenesis

status: Public on Mar 25 2021

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

institute: Lund University

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Patient-derived organoids after neoadjuvant FOLFIRINOX predict therapy resistance in pancreatic ductal adenocarcinoma

status: Public on Mar 23 2021

city: Rotterdam

first: Jiang

last: Chang

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: Pancreatic ductal adenocarcinoma is an extreme lethal cancer with a poor treatment response to all the current chemotherapies. We generated a library of PDAC organoid lines from resected tumors, five from treatment-naive patients and five from patients who received neoadjuvant FOLFIRINOX (eight cycles). We assessed weather residual cancer cells in the tumor lesions of the patients treated with neoadjuvant FOLFIRINOX developed resistance to the treatment. Further we perfromed transcriptome analysis to investigate: 1- weather organoids recapitualting their corresponding tumor tissue 2- To investigate any modifications in the expression of the genes inflicted by FOLFIRINOX treatment.

overall_design: We generated ten PDAC organoid lines, five from treatment-naive patients and five from patients who received neoadjuvant FOLFIRINOX (eight cycles). We first assessed the histological, genetic, and transcriptional characteristics of the organoids and their matched primary PDAC tissue. We evaluated the treatment response characteristics of the organoids to single agents of the FOLFIRINOX regimen —(i.e., 5-FU, irinotecan, and oxaliplatin). Finally, we used global mRNA-seq analyses to identify FOLFIRINOX resistance pathways.

first: Farshadi

last: Aida


title: The Card19 locus regulates apoptosis and pyroptosis downstream of caspase activation and gasdermin D cleavage independently from IL-1 cytokine release

status: Public on Mar 21 2021

city: Philadelphia

first: Rina

last: Matsuda

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

summary: Cell death plays a critical role in inflammatory responses. During pyroptosis, inflammatory caspases cleave Gasdermin D (GSDMD) to release an N-terminal fragment that generates plasma membrane pores that mediate cell lysis and IL-1 release. However, certain stimuli and cell types release IL-1 cytokines through GSDMD pores in cells that remain viable, a process termed hyperactivation. How these distinct cell fate choices are regulated downstream of GSDMD pore formation is unknown. Here, we demonstrate that the Card19 locus promotes lysis downstream of caspase activation. Despite being largely protected from cell death, CARD19-deficient macrophages had no defect in caspase activation, IL-1 secretion, or GSDMD cleavage. CARD19, a mitochondrial protein, was not responsible for the observed phenotypes, nor was the recently identified pore forming protein NINJ1 which regulates terminal pore formation during multiple forms of cell death. Furthermore, previously identified cell death phenotypes attributed to Sterile alpha and heat Armadillo motif-containing protein (SARM) were revealed to be caused by a passenger mutation. Importantly, Card19-/ mice had increased susceptibility to Yersinia infection, including increased mortality, higher bacterial burdens and pronounced splenomegaly. These findings implicate the Card19 locus as a factor that couples caspase processing and GSDMD cleavage to cell death, providing insight into how the checkpoint between hyperactivation and cell death is regulated.

overall_design: Total 11 samples. Three technical replicates were analyzed for four groups (two genotypes, with or without LPS). Sample 7 was lost during processing and was not included in analysis.

first: Elisabet

last: Bjanes

first: Reyna

middle: G

last: Sillas

first: Timothee

last: Fettrelet

first: Benjamin

last: Demarco

first: Alexandra

last: DeLaney

first: Eric

middle: M

last: Lopez

first: Daniel

last: Grubaugh

first: Meghan

last: Wynosky-Dolfi

first: Naomi

last: Philip

first: Dorothy

last: Tovar

last: Beiting

first: Leonel

last: Joannas

first: Brian

last: Schaefer

first: Jorge

last: Henao-Mejia

first: Kaiwen

last: Chen

first: Petr

last: Broz

first: Igor

last: Brodsky


title: Next Generation Sequencing Analysis of USP2-AS1_KD A549 cell line

status: Public on Mar 19 2021

city: Hefei

first: Guang

last: Zhang

state: Anhui

address: 443 Huangshan Road, Shushan District

department: School of Basic Medical Sciences, Division of Life Sciences and Medicine

institute: university of science and technology of China

summary: The goals of this study are to find target genes of USP2-AS1 and to investigate witch pathway it can regulate in A549 cell line

overall_design: A549 RNA profiles of shctrl and shUSP2-AS1

first: Bingyan

last: Li

first: Chenfeng

last: Wang


title: Transcriptional control of HP1a by the RNA binding proteins RBMX/L1 maintain chromatin state in myeloid leukemia

status: Public on Mar 18 2021

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

summary: RNA binding proteins (RBPs) are key arbiters of post-transcriptional regulation that have been found to be dysregulated in hematological malignancies. Here, we identify the RBP RBMX and its retrogene RBMXL1 to be required for murine and human myeloid leukemogenesis. RBMX/L1 are overexpressed in acute myeloid leukemia (AML) primary patients compared to healthy individuals, and RBMX/L1 loss delayed leukemia development. Complex chromosomal karyotyping analysis and assay for transposase-accessible chromatin sequencing demonstrated that RBMX/L1 loss led to significant changes in chromatin accessibility and compaction. We found that RBMX/L1 directly binds to mRNAs and affects transcription of multiple loci, including the heterochromatin protein 1 alpha (HP1a) mRNA. Using single molecule resolution RNA fluorescence in situ hybridization, we uncovered that RBMX/L1 controls the nascent transcription of the HP1a locus. Forced HP1a expression rescued the RBMX/L1 depletion effects on cell growth and apoptosis. Overall, we determine that RBMX/L1 control leukemia cell survival by regulating chromatin state through its downstream target HP1a. These findings illuminate a novel mechanism for RBPs directly promoting transcription and suggest RBMX/L1 as well as HP1a as potential novel therapeutic targets in myeloid malignancies.

overall_design: 21 human cell line samples,with RBMX/L1 KD and controls

first: Camila

last: Prieto

first: Diu

last: Nguyen

first: Michael

last: Kharas

first: Alexandar

last: Perez


title: Muscle fibrosis in chronic kidney disease

status: Public on Mar 01 2021

city: North Chicago

first: Ameya

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

summary: Patients with chronic kidney disease (CKD) are at markedly increased risk of disability, hospitalization, and death. Impaired physical function, which is common in CKD, is a major risk factor for these poor outcomes. CKD patients perform substantially below age-predicted norms on a variety of clinically relevant physical performance tests. Altered muscle physiology is an important cause of these functional deficits. We recently described skeletal muscle fibrosis in the vastus lateralis muscle of patients with severely impaired kidney function. Greater severity of fibrosis was associated with lower leg extension strength and reduced endurance capacity, suggesting that muscle fibrosis in CKD patients is functionally significant. An important unanswered question is whether muscle fibrosis in CKD is a slowly progressive process beginning with early loss of kidney function, or a complication observed only with severe disease. Here, we examined the associations of estimated glomerular filtration rate (a measure of kidney function) with measures of fibrosis across a broad range of kidney function, and tested the effect of receiving treatment with dialysis. We also integrated muscle transcriptomic analyses to provide further insight into this novel aspect of muscle pathology in CKD.

overall_design: The subject population of this study has been previously described [PMID: 30280599]. Subjects were recruited from a prospective cohort study of CKD patients not receiving dialysis treatment at the time of recruitment (estimated glomerular filtration rate [eGFR] <30 ml·min−1·1.73 m−2). Eligible patients were ≥21 years of age and competent to provide informed consent for study participation. Exclusion criteria included lower extremity amputation, use of immunosuppressive medication in the previous 3 mo, and current cancer diagnosis and/or treatment.

first: Matthew

middle: K

last: Abramowitz

first: Camille

last: Brightwell

first: Christopher

last: Fry


title: Quantitative Analysis of Scramble control and LncRNA HMRHL siRNA knockdown in chronic myelogenous leukemia (CML) K562 Cell lines transcriptome profile

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary: The goals of this study are to compare differentianl gene expression between Scramble control and knockdown of HMRHL in K562 cell lines. Subsequently to determine the cellular pathway and biological process affected most upon HMRHL silencing from NGS-derived K562 cells transcriptome profiling (RNA-seq).

overall_design: K562 cells mRNA profiles of scramble control and HMRHL knockdown were generated by deep sequencing, in duplicate, using Illumina HiSeq.

first: Subhendu

last: Choudhury

first: Sangeeta

last: Dutta

first: Utsa

last: Bhaduri

first: Satyanarayana

last: Rao


title: Systematic Phenotyping and Characterization of the 5xFAD mouse model of Alzheimer’s Disease

status: Public on Mar 04 2021

city: Irvine

first: Narges

last: Rezaie

state: California

address: 2218 Biological Sciences III

institute: University of California, Irvine

summary: we conducted a detailed phenotypic characterization of the 5xFAD model on a congenic C57BL/6J strain background, across its lifespan – including a seldomly analyzed 18-month old time point to provide temporally correlated phenotyping of this model and a template for characterization of new models of LOAD as they are generated. This comprehensive analysis included quantification of plaque burden, Aβ biochemical levels, and neuropathology, neurophysiological measurements and behavioral and cognitive assessments, and evaluation of microglia, astrocytes, and neurons. Analysis of transcriptional changes was conducted using bulk-tissue generated RNA-seq data from microdissected cortices and hippocampi as a function of aging, which can be explored at the UCI Mouse Explorer and AD Knowledge Portal. This deep-phenotyping pipeline identified novel aspects of age-related pathology in the 5xFAD model.

overall_design: Bulk RNA-seq of 4 different time point(4,8,12,18 month) in two brain regoins (hippocampus and cortex) and two strains (5xFAD and BL6)

first: Ali

last: Mortazavi


title: Circulating miR-181 is a prognostic biomarker for amyotrophic lateral sclerosis

status: Public on Mar 12 2021

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

summary: We report that high levels of miR-181, a miRNA enriched in neurons of the brain and spinal cord, predicts a >2 fold risk of death in ALS patients

overall_design: We tested miRNAs for prognostic value in a discovery cohort of 126 patients, and then validated our findings in an independent replication cohort (additional 122 patients).

first: Nancy

last: Yacovzada

first: Eran

last: Yanowski

first: Anna

last: Coenen-Stass

first: Julian

last: Grosskreutz

first: Ching-Hua

last: Lu

first: Linda

last: Greensmith

first: Andrea

last: Malaspina

first: Pietro

last: Fratta

last: Hornstein


title: N1-methyladenosine methylations in tRNA drive liver tumorigenesis by PPARδ-mediated cholesterol synthesis

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

summary: Increased protein translation plays a critical role in cancer development and treatment1,2. However, the molecular mechanism that is involved in this process remains poorly understood. N1-methyladenosine (m1A) methylation in RNA accounts for regulating mRNA translation in a post-transcriptional manner3,4. Here we show that m1A methylation levels are remarkably elevated in hepatocellular carcinoma (HCC) patient tumor tissues, especially in patients with microscopic vascular invasion (MVI). Moreover, m1A methylation signals are increased in liver cancer stem cells (CSCs) and are negatively correlated with HCC patient survival. Consistently, TRMT6 and TRMT61A, forming m1A methyltransferase complex, are highly expressed in advanced HCC tumors and are negatively correlated with HCC survival. TRMT6/TRMT61A-mediated m1A methylations are required for self-renewal of liver CSCs and tumorigenesis. Mechanistically, TRMT6/TRMT61A-dependent m1A in tRNA boost PPARδ expression, which triggers cholesterol synthesis to activate Hedgehog signaling, driving self-renewal of liver CSCs and tumorigenesis. For potential therapeutic benefit, we further identify a specific inhibitor against TRMT6/TRMT61A complex that exerts effective therapeutic effect on liver cancer with high m1A methylations. Our findings provide novel insights into the function and molecular mechanism of m1A modifications underlying liver tumorigenesis and drug target, which will serve as a new biomarker for HCC and pave a new way to develop more effective therapeutic strategies for HCC patients.

overall_design: We find that the overall m1A methylation signal as well as the relevant m1A-methyltransferase TRMT6/61A are of abberrently high level in HCC tumor samples. By performing m1A sequencing for small RNA populations, we discovered several tRNAs with elevated m1A58 methylation stoicheometry. Then we evaluate the influenences on gene expression via Ribo-seq, and proved that TRMT6/TRMT61A-dependent m1A in tRNA boost expression of some metabolic pathway genes, which trigger cholesterol synthesis to activate Hedgehog signaling, driving self-renewal of liver CSCs and tumorigenesis.

first: Yanying

last: Wang

first: Xiaoyu

last: Li

first: Chengqi

last: Yi

first: Zusen

last: Fan


title: An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feedback Interactions [methylation]

status: Public on Feb 25 2021

city: Barcelona

first: Ana

last: Sevilla

state: Barcelona

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

department: Departamento de Biologia Celular, Fisiologia e Inmunologia

country: Spain

institute: Universidad de Barcelona

type: Methylation profiling by genome tiling array

summary: Cell fate decisions during development are governed by multi-factorial regulatory mechanisms including chromatin remodelling, DNA methylation, binding of transcription factors to specific loci, RNA transcription and protein synthesis. However, the mechanisms by which such regulatory 'dimensions' coordinate cell fate decisions are currently poorly understood. Here we quantified the multi-dimensional molecular changes that occur in mouse embryonic stem cells (mESCs) upon depletion of Estrogen related receptor beta (Esrrb), a key pluripotency regulator. Analyses of coordinated expression changes identified strikingly different epigenetic regulatory patterns of pluripotency and differentiation states. Comparative analyses of expression changes subsequent to depletion of Esrrb or Nanog, indicated that a system of interlocked feed-forward loops involving both factors plays a central part in regulating the timing of mESC fate decisions. Taken together, our meta-analyses support a hierarchical model in which pluripotency is maintained by an Oct4-Sox2 regulatory module, while the timing of differentiation is regulated by a Nanog-Esrrb

overall_design: Total of 24 samples; Esrrb day0 (+Dox_TF expressed), Esrrb kd day1, Esrrb kd day3, Esrrb kd Day5, Nanog day0 (+Dox_TF expressed), Nanog kd day1, Nanog kd day3 and Nanog kd day5; all performed in triplicates. Nimblegen MM9HX3 methylation profiles in mouse embryonic stem cell (mESCs)  in the presence of  Esrrb (day0) or upon knockdown of Esrrb at different time points day1, day3 and day5 and in the presence of Nanog (day0) or upon knockdown of Nanog at different time points day1, day3 and day5.

first: Dimitri

last: Papatsenko

first: Amin

last: Mazloom

first: Huilei

last: Xu

last: Vasileva

first: Richard

last: Unwin

first: Gary

last: LeRoy

first: Edward

last: Chen

first: Francine

last: Garrett

first: Dung-Fang

last: Lee

first: Benjamin

last: Trinite

first: Ryan

middle: L

last: Webb

first: Zichen

first: Jie

last: Su

last: Gingold

first: Ari

last: Melnick

last: Garcia

first: Anthony

last: Whetton

first: B

last: MacArthur

first: Avi

last: Ma’ayan

first: Ihor

last: Lemischka


title: An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feedback Interactions [gene expression]

first: Ana

last: Sevilla

overall_design: Total of 12 samples; Esrrb day0, Esrrb kd day1, Esrrb kd day3 and Esrrb kd Day5; all performed in triplicates. Affymetrix GeneChip® Mouse Gene 1.0 ST arrays  analyses of mouse embryonic stem cell gene expression profiles in the presence of  day0 or upon knockdown of Esrrb at different time points day1, day3 and day5

first: Dimitri

last: Papatsenko

last: Mazloom

last: Xu

last: Wang

first: Julian


title: Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids

status: Public on Feb 23 2021

city: Raleigh

first: Albert

middle: J

last: Keung

state: NC

address: 911 Partners Way

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Here, we used agarose microwells to control embryos body (EB) shapes and generated whole brain human cerebral organoids (hCO) from these EBs to investigate the effects of early spatial regulation on transcriptomic changes during brain region specification using bulk RNA sequencing. Our results showed that gross morphological and transcriptional changes related to hCO differentiation were similar between 96-well and microwell hCOs, indicating that the microwell growth environment did not significantly affect the overall neural differentiation or viability of the hCOs. However, investigating individual developmental time points and comparing across 96-well and microwell conditions more closely revealed notable differences in genes associated with pluripotency, mesoderm, MGE, retina and cortical development, and epithelial and mesenchymal fates, implying that the microwell growth environment may bias lineage commitment in neurodevelopment.  Furthermore, we found that the direction and intensity of this transcriptional bias was associated with the starting EB shapes. The butterfly shape showed the most noticeable differences, followed closely by the peanut shape. Among other notable differences, round microwells exhibited a potential delay in the kinetics of neurodevelopment, and our results also demonstrated that non-spherical shapes may favor the development of MGE-associated brain regions and cell types over cortical regions.

overall_design: Investigation of the affects of four different microwell shapes on the development of whole brain human cerebral organoids at three different time points.

first: Dilara

last: Sen

first: Alexis

last: Voulgaropoulos


title: An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feedback Interactions [ChIP-seq]

overall_design: Genome-wide study of Esrrb  binding sites. Examination of 2 different histone modifications in a time series after Esrrb knockdown.

first: Amin

first: Huilei

last: Vasileva

first: Richard

last: Unwin

first: Gary

last: LeRoy

first: Edward

last: Chen

first: Francine

last: Garrett

last: Lee

last: Trinite

last: Webb


title: RNA-seq analysis in fibroblast IMR90 CTRL/MYC/MYC+SF3A3 KD

first: Phuong

last: Cao Thi Ngoc

summary: Splicing is a central RNA-based process commonly altered in human cancers; however, how the splicing machinery is co-opted during tumorigenesis remains largely unresolved. Here we identify the splice factor SF3A3 at the nexus of an oncogenic translation program that rewires splicing to promote tumorigenesis. Our results suggest that key spliceosomal networks centered on the essential core U2-associated factor, SF3A3, are exquisitely controlled at the translation level during oncogenic stress. Upon oncogene activation, SF3A3 translation is rapidly enabled via a conserved internal stem-loop structure embedded in the transcript 5’ untranslated region (UTR). Uncoupled SF3A3 translation leads to alternative splicing of several mRNAs involved in mitochondrial dynamics, and induces a metabolic switch that fuels cancer initiation properties in MYC-driven breast tumorigenesis in vivo. Finally, we compelling show that SF3A3 is post-transcriptionally altered and predicts for poor prognosis in aggressive triple negative breast cancers. Together, these findings unveil a highly dynamic regulatory network that interfaces mRNA splicing and translation to orchestrate cancer gene expression networks.

overall_design: 3 sets of samples including control (CTRL) or MYC overexpressing cells with short hairpin control (MYC) or short hairpin targeting SF3A3 (MYC+SF3A3 KD) were included in the study. Each sample was prepared in the biologically independent, matched triplicates.

first: Maciej

last: Ciesla

first: Danny

last: Incarnato

first: Cristian

last: Bellodi


title: Next generation sequencing facilities quantitative analysis of human oropharyngeal squamous cell carcinoma, small cell carcinoma and non-cancerous tonsil tissue.

status: Public on Feb 16 2021

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

summary: To investigate the differences of transcriptional activities between oropharyngeal squamous cell caricnoma and small cell carcinoma, we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq).

overall_design: Total RNA extracted from non-cancerous tissue (Norrmal), squamous cell carcinoma (SqCC) and small cell carcinoma (SmCC) derived from a 53-years old female patient with oropharyngeal carcinoma were subjected to RNA-seq analysis. The sequencing libraries genetrated from RNA were analyzed by DNBSEQ-G400.

first: Muneyuki

last: Masuda

first: Takashi

last: Nakagawa


title: Characterization of immune cells from an ICB responder and non-responder using scRNA-seq

status: Public on Feb 08 2021

city: Chicago

first: Weiguo

last: Cui

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: There is a strong correlation between myeloid derived suppressor cells (MDSCs) and resistance to immune checkpoint blockade (ICB), but the detailed  underlying this correlation are largely unknown. Using single-cell RNA-seq analysis in a bilateral tumor model, we found that immunosuppressive myeloid cells with characteristics of fatty acid oxidative metabolism dominate the immune-cell landscape in ICB-resistant subjects. In addition, we uncovered a previously underappreciated role of a serine/threonine kinase, PIM1, in regulating lipid oxidative metabolism via PPARγ-mediated activities. Enforced PPARγ expression sufficiently rescued metabolic and functional defects of Pim1-/- MDSCs. Consistent with this, pharmacological inhibition of PIM kinase by AZD1208 treatment significantly disrupted myeloid cell–mediated immunosuppression microenvironment and unleashed CD8+ T cell–mediated antitumor immunity, which enhanced PD-L1 blockade in preclinical cancer models. PIM kinase inhibition also sensitized non-responders to PD-L1 blockade by selectively targeting suppressive myeloid cells. Overall, we have identified PIM1 as a metabolic modulator in MDSCs that is associated with ICB resistance and can be therapeutically targeted to overcome ICB resistance.

overall_design: Two samples (2 days after last doasage of anti-PD-L1 therapy) were prepared using 10x Genomics Chromium platform

first: Gang

last: Xin

first: Yao


title: CircARHGAP12 triggers MSC autophagy to facilitate its effect on repairing diabetic wounds by sponging miR-301b-3p/ATG16L1 and miR-301b-3p/ULK2

status: Public on Mar 15 2021

city: Yiwu

first: Qiang

last: Sun

address: No. N1, Shangcheng Avenue

summary: Circular RNAs (circRNAs) have been found to play critical roles in the development and progression of human diseases. However, the role of circRNAs in regulating MSCs (mesenchymal stromal cells) to repair diabetic wounds remains unclear. Here, we showed that MSCs subjected to high glucose stress showed an obvious decrease in circARHGAP12, while circARHGAP12-mediated autophagy inhibited high glucose-induced apoptosis of MSCs. Mechanistically, circARHGAP12 could directly interact with miR-301b-3p, and subsequently act as a miRNA sponge to regulate the expression of the miR-301b-3p target genes ATG16L1 and ULK2 and the downstream signaling pathway. Furthermore, circARHGAP12 led to a decrease in apoptosis of MSCs in wounds and promoted wound healing. Taken together, these data indicated that circARHGAP12/ miR-301b-3p/ATG16L1 and ULK2 regulatory networks may be a potential therapeutic target for MSCs in repairing diabetic wounds.

overall_design: To generate a circRNA profiling database, high glucose induced MSCs and control MSCs were selected for circRNA analysis.

last: Li


title: Genome-wide map of cohesin positions in RT112 bladder cancer cells

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

summary: Bladder cancer is one of the most common genitourinary malignancies worldwide. It is a heterogeneous disease at the clinical, pathological, and genetic levels.   In an exome-sequencing study of bladder cancer, we identified genes mutated in bladder cancer coding for proteins involved in chromatin modification, cell division, and DNA repair. STAG2, a constituent of the cohesin complex, was commonly mutated or lost, mainly in tumors of low stage or grade. Loss of STAG2 expression was often observed in genomically stable tumors, suggesting that STAG2 may act as a tumor suppressor through mechanisms other than chromosome segregation (Balbás-Martínez et al. 2013). In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and organization of the genome into Topologically Associating Domains (TADs). Two variant cohesin complexes that contain either STAG1 or STAG2 are present in all cell type. Here we addressed their genome wide binding in bladder cancer cells.

overall_design: ChIPseq of STAG1, STAG2 and SMC1a (common cohesin component) binding sites in chromatin from RT112 bladder cancer cells.

first: Eleonora

last: Lapi

first: F

middle: X

last: Real


title: Expression data from mouse liver after chow and high-fat diet feeding

status: Public on Jan 31 2021

city: Lübeck

first: Henriette

last: Kirchner

address: Ratzeburger Allee 160

department: Institute for Human Genetics

country: Germany

institute: University of Lübeck

summary:
Epigenetic changes are present in multiple tissues of rodents and subjects suffering from obesity and type 2 diabetes.  Especially, genes that are important for glucose and lipid metabolism seem to be at least co-regulated by DNA methylation. We aimed to investigate if altered DNA methylation in liver of mice can be induced by feeding a high-fat diet and if these changes can be reverted by weight loss.
We used microarrays to measure the hepatic gene expression pattern in chow and high-fat diet (HFD) fed mice to identify dysregulated pathways which contribute to diet-induced obesity and insulin resistance. DNA methylation was measured of candidate genes to evaluate this as potential regulatory mechanism.

overall_design: Liver tissue of HFD and chow fed mice was collected after one week and twelve weeks of feeding for RNA extraction and hybridization on Affymetrix microarrays. This longitudinal design allows us to preselect dysregulated pathways in the manifestation of obesity and insulin resistance. Thereby, identified candidate genes are used for a close tracking of the expression pattern over a time course of 12 weeks to identify possible metabolic switches in liver and to assess whether this is causal or consequential of HFD feeding. DNA methylation was measured at selected potential regulatory CpG-sites in order to evaluate this mechanism as key regulator of altered gene expression.

first: Cathleen

last: Geißler

first: Christin

last: Krause

first: Anne-Marie

last: Neumann

first: Martina

last: Grohs

first: Meike

last: Kähler

first: Ingolf

last: Cascorbi

first: Alfor

last: Lewis

first: Randy

last: Seeley

first: Henrik

last: Oster


title: Generalized reversal of glial and neurovascular cell transcriptomic aging signatures by glucagon-like peptide-1 receptor agonist

city: Hong Kong

first: Ho

last: Ko

address: 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

institute: The Chinese University of Hong Kong

summary: Pharmacological reversal of brain aging is a long-sought yet challenging strategy for the prevention and treatment of age-related neurodegeneration, due to the diverse cell types and complex cellular pathways impacted by the aging process. Recently, we demonstrated that brain endothelial cell (EC) aging is transcriptomically and functionally reversible by treatment with exenatide, a glucagon-like peptide-1 receptor (GLP-1R) agonist (GLP-1RA)(1). Here, we report that the reversal of transcriptomic aging signatures by GLP-1RA treatment is a generalized phenomenon in multiple major brain cell types, including glial (including astrocyte (AC), oligodendrocyte precursor cell (OPC), microglia (MG) and oligodendrocyte (OLG)) and mural (i.e. pericyte (PC) and smooth muscle cell (SMC)) cells. The age-related expression changes ameliorated by GLP-1RA encompass cell type-shared and specific functional pathways implicated in aging and neurodegeneration. These results show the feasibility of brain ageing reversal by pharmacological means, provide mechanistic insights into the neurological benefits of GLP-1RAs in diabetic patients(2, 3), and imply that GLP-1RA may be a generally applicable pharmacological intervention for non-diabetic patients at risk of age-related neurodegeneration.

overall_design: Three mouse brain samples with 10X genomic single cell sequencing

first: Zhongqi


title: Selectivity of mRNA degradation by autophagy in yeast

status: Public on Mar 08 2021

city: Yokohama

first: Shiho

last: Makino

address: 4259-S2-12 Nagatsuta-cho, Midori-ku

country: Japan

institute: Tokyo Institute of Technology

summary: Synthesis and degradation of cellular constituents must be balanced to maintain cellular homeostasis, especially during adaptation to environmental stress. The role of autophagy in the degradation of proteins and organelles is well-characterized. However, autophagy-mediated RNA degradation in response to stress and the potential preference of specific RNAs to undergo autophagy-mediated degradation have not been examined. In this study, we demonstrate selective mRNA degradation by rapamycin-induced autophagy in yeast. Profiling of mRNAs from the vacuole reveals that subsets of mRNAs, such as those encoding amino acid biosynthesis and ribosomal proteins, are preferentially delivered to the vacuole by autophagy for degradation. We also reveal that autophagy-mediated mRNA degradation is tightly coupled with translation by ribosomes. Genome-wide ribosome profiling suggested a high correspondence between ribosome association and targeting to the vacuole. We propose that autophagy-mediated mRNA degradation is a unique and previously-unappreciated function of autophagy that affords post-transcriptional gene regulation.

overall_design: Ribosome profiling and RNA-seq

first: Tomoko

last: Kawamata

first: Shintaro

last: Iwasaki

first: Yoshinori

last: Ohsumi


title: Cell-type specific multi-QTL analyses of cultured human primary melanocytes

status: Public on Feb 04 2021

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

type:
Methylation profiling by array
SNP genotyping by SNP array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Modulation of inflammation and parasite infection by cinnamaldehyde

status: Public on Jan 23 2021

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: In vivo and in vitro experiments were conducted to assess how cinnamaldehyde impacts on immunity to infection.

overall_design: In a 2x2 factorial design, C57BL/6 mice were either infected with Heligmosomoides polygyrus (Hp) or not, and fed either cinnamaldehyde (CA) or a control diet. In addition, CMT93 murine epithelial cells were exposed in vitro to CA.


title: Aberrant RNA methylation triggers recruitment of an alkylation repair complex

status: Public on Feb 01 2021

city: St. Louis

first: Nima

last: Mosammaparast

state: MO

address: 660 S Euclid Ave

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: Central to genotoxic responses is their ability to sense highly specific signals to activate the appropriate repair response. We previously reported that the activation of the ASCC-ALKBH3 repair pathway is exquisitely specific to alkylation damage in human cells. Yet the mechanistic basis for the selectivity of this pathway was not immediately obvious. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. In turn, recruitment of ASCC during alkylation damage, which is mediated by the E3 ubiquitin ligase RNF113A, suppresses transcription and R-loop formation. We further show that alkylated pre-mRNA is sufficient to activate RNF113A E3 ligase in vitro in a manner dependent on its RNA binding Zn-finger domain. Together, our work identifies an unexpected role for RNA damage in eliciting a specific response to genotoxins.

overall_design: Role for RNA damage in eliciting a DNA repair response by the ASCC complex

first: Ning

last: Tsao

first: Joshua

last: Brickner

first: Rebecca

last: Rodell

first: Adit

last: Ganguly

first: Matthew

last: Wood

first: Clement

last: Oyeniran

first: Tanveer

last: Ahmad

first: Hua

last: Sun

first: Albino

last: Bacolla

first: Lisheng

first: Valentina

last: Lukinovic

first: Jennifer

last: Soll

first: Brittany

last: Townley

first: Alexandre

last: Casanova

first: John

last: Tainer

first: Chuan

last: He

first: Alessandro

last: Vindigni

first: Nicolas

last: Reynoird


title: Estrogen Drives Melanocortin Neurons To Reduce Sedentary Behavior

city: Boston

first: Bruno

last: Gegenhuber

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Estrogen depletion in both rodents and humans leads to inactivity, unhealthy fat accumulation, and metabolic syndrome, underscoring the conserved metabolic benefits of estrogen signaling that inevitably decline with aging. Here, we uncover a hypothalamic node that integrates estrogen and melanocortin-4 receptor (MC4R) signaling to drive episodic bursts in activity prior to ovulation. Skirting the estrogen-dependent gating of this node by CRISPR activation of Mc4r reduces sedentary behavior long-term in both males and females. Our findings expand the impact of MC4R signaling beyond food intake regulation and rationalize reported sex-differences in melanocortin signaling including increased disease severity for women with MC4R-insuffciency. This newly identified hormone-dependent activity node illustrates the potency of estrogen in maintaining an active lifestyle.

overall_design: Analysis of ERα binding in adult mouse limbic tissue by CUT&RUN

first: William

middle: C

last: Krause

first: Ruben

last: Rodriguez

first: Navneet

last: Matharu

first: Andreas

first: Adriana

last: Padilla

first: Candice

last: Herber

first: Stephanie

last: Correa

first: Nadav

last: Ahituv

first: Jessica

last: Tollkuhn

first: Holly

last: Ingraham


title: Multi-omics analysis to study hepatitis B virus-host interaction

status: Public on Mar 06 2021

city: Shanghai

first: Menghuan

last: Zhang

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

summary: Curing treatment for HBV infection is yet unavailable, mainly due to unmet gaps in current understanding of the details about HBV-host interaction. By quantitatively assessing HBV-induced global changes in host transcriptome, translatome and proteome, we identified multiple previously unknown transcriptional and translational events that HBV orchestrated to remodel host proteostasis networks and afford micro-environments essential for HBV proliferation and persistence.By delineating novel drug targets and biomarkers in HBV-host interaction, multi-omics interrogation may facilitate the development of next-generation therapeutics or diagnostics against HBV infection and the related maladies.

overall_design: Examination of transcriptome, translatome and proteome in HBV positive or HBV negative conditions

first: Ronggui

last: Hu

first: Shilin

last: Yuan

first: Guanghong

last: Liao

first: Yuanfei

last: Zhu


title: Prolonged epigenetic and synaptic plasticity alterations following single exposure to a psychedelic in mice

status: Public on Feb 24 2021

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

summary: We examined the effects of the psychedelic drug amphetamine 1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane (DOI) on the epigenomics and transcriptomics in mouse frontal cortex.

overall_design: We conducted ChIP-seq (H3K27ac) and RNA-seq on neurons (NeuN+ fraction) from control mouse brains (mice with only vehicle injection,VEH) and treated mouse brains (24 hours (24h), 48 hours (48h), and 7 days (7d) after amphetamine (2,5-dimethoxy-4-iodoamphetamine [DOI] injection). In these experiments, the frontal lobe of the mouse cortex (anterior to bregma +1 mm) was examined. Each treatment group contained 6 mice. Two replicates were produced on each brain sample for each assay. ChIP-seq data were generated using MOWChIP-seq (Zhu et al., Nature Protocols 14 (2019) 3366-3394.) and RNA-seq data were produced using the combination of SMART-seq2 (Picelli et al., Nature Protocols 9 (2014) 171–181.) and a Nextera XT DNA library preparation kit. The filename contains the information on the experimental group, the number of the mouse within the group, the nubmer of replicate, and the epigenomic/transcriptomic data set (either H3K27ac or mRNA). For example, "VEH1-1-K27ac" refers VEH group mouse 1, replicate 1 ChIP-seq data on H3K27ac.

first: Bohan

first: Zirui

last: Zhou


title: An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions.

first: Ana

last: Sevilla


title: Predictive potential of circulating Ube2h mRNA as an  E2 ubiquitin-conjugating enzyme for diagnosis or treatment of Alzheimer’s disease

status: Public on Dec 31 2020

city: Daegu

first: Jae-Yeol

last: Joo

address: 61, cheomdan-ro, Dong-gu,

country: South Korea

institute: Korea Brain Research Institute

summary: Neurodegenerative disorders are status in which neuronal cell death, miscommunications between synapse, and abnormal accumulation of proteins in the brain. Alzheimer’s disease (AD) is one of the age-related disorders which is most common degenerative disorders today, and strongly involved memory consolidation and cognitive in the brain. Amyloid-β and tau proteins are trigger for AD pathogenesis, and usually use for AD candidate biomarkers in the clinical research. Especially, clinical exam, brain imaging and molecular biological methods are being used to diagnosis for AD. Genome-wide association study (GWAS) is new biomedical method, and use contribute to understanding of many human diseases included brain diseases. Here, we identified ubiquitin conjugating enzyme E2 (Ube2) gene expression in the neuron through GWAS. The subfamilies of Ube2 genetic expression and inborn errors affect ubiquitin proteasome system (UPS) leading to protein degradation in the brain. We found that only Ube2h mRNA transcription was significantly increased in the blood from AD, however we did not find change of Ube2 subfamily genes expression in the blood and brain tissue. These data may provide information of diagnosis or clinical approach, and suggest that cell-free circulating Ube2h mRNA is novel potential biomarker for AD.

overall_design: Examination of Ube2 submailies gene expression profiling from 5xFAD mouse brain and blood.

first: Key-Hwan

last: Lim


title: miRNA profiling of putative biomarker candidates in Mycobacterium avium subsp. paratuberculosis-infected cattle

status: Public on Feb 05 2021

city: Seoul

first: Sungwoon

last: Choi

state: Gwanak-gu

address: 1. Gwanak-ro

department: Veterinary Medicine

institute: Seoul National University

summary: Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s disease that is a chronic wasting disease in ruminants. Spread of MAP is mainly provoked by a long subclinical stage during which MAP is shed into the environment with feces; accordingly, detection of subclinical animals is very important to its control. Therefore, the current diagnostic methods are not suitable for detection of subclinical animals. In this study, we conducted to develop a diagnostic method for analysis of the expression of genes of prognostic potential biomarker candidates in cattle naturally infected with MAP. We conducted miRNA-Seq to evaluate potential biomarker candidates. Experimental animals were divided into four groups based on fecal MAP PCR, serum ELISA, and clinical sign.

overall_design: miRNA-Seq were analyzed in four groups divided into fecal MAP PCR, serum ELISA, and clinical sign.

first: Sung

middle: W

first: Han

middle: S

last: Yoo


title: RNA-sequencing experiments comparing P0 control and RXRG/RARb double mutants frontal cortex

status: Public on Jan 01 2021

city: New Haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

summary: To understand the functional significance of RA signaling through the RXRG/RARB heterodimer in the developing cortex, we performed RNA-seq experiments comparing different regions of the P0 mouse frontal cortex (mPFC, secondary motor cortex (MOs)/ primary motor cortex (MOp), and OFC ) in Rarb and Rxrg dKO and WT littermate controls.

overall_design: Freshly dissected P0 brains were frozen at -80C, and moved to RNALater 12-16 hrs prior to further dissection. Medial frontal, motor, and orbitofrontal regions were microdissected. RNA was isolated using Rneasy plus micro kit (Qiagen), and cDNA libraries were created using SMART-seq v4 Ultra Low Input Kit (Takara) and Nextera XT DNA library Prep Kit (Illumina). Libraries were normalized and sequenced at the Yale Center for Genomic Analysis (YGCA) using the NovaSeq with 100 bp paired end reads.

first: Kartik

last: Pattabiraman

first: Belen

last: Lorente-Galdos


title: Gene expression of SARS-CoV-2-infected Vero E6 cells with remdesivir treatment

status: Public on Feb 02 2021

city: Bethesda

first: Eytan

last: Ruppin

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: RNA sequencing was performed on control and SARS-CoV-2 infected Vero E6 cells, with or without remdesivir treatment to study the biological changes after SARS-CoV-2 infection and to evaluate the effectiveness of remdesivir on the gene expression level. 500,000 Vero E6 cells were seeded in 6-well plates. The following day, the cell medium was replaced with fresh medium supplemented with either DMSO or 1 µM remdesivir, and cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI=0.3), with three replicates per experimental condition. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

overall_design: mRNA profiles of control (mock-infected) and 24h post-SARS-CoV-2-infection Vero E6 cells with or without 1 µM remdesivir treatment with three replicates per condition.

first: Riva

last: Laura

first: Cheng

last: Kuoyuan

first: Chanda

last: Sumit

first: Ruppin

last: Eytan


title: RNA-seq: Loss of a heterochromatin anchor rescues altered genome organization and EDMD muscle defects triggered by a laminopathy mutation

city: Basel

first: Susan

last: Gasser

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: Point mutations in nuclear structural protein lamin A produce rare,  tissue-specific diseases called laminopathies. The introduction of a  human Emery Dreifuss Muscular Dystrophy (EDMD)-inducing mutation (lamin  A-Y45C) into C. elegans lamin (LMN-Y59C), recapitulates many EDMD  phenotypes, and correlates with hyper-sequestration of heterochromatic  arrays at the nuclear periphery. Using muscle-specific emerin Dam-ID, we  also document the misorganization of endogenous chromatin in the  LMN-Y59C mutant. We score increased perinuclear positioning along  chromosome arms, and enhanced release within chromosomal cores.  Coincidentally, Y59C worms have reduced locomotion and compromised  sarcomere integrity. By coupling the Y59C mutation with deletion of the  perinuclear chromodomain protein CEC-4, which tethers H3K9-methylated  chromatin, we rescue the EDMD-like physiology and ultrastructural  defects in sarcomeres. Deletion of cec-4 also rescued the Y59C-induced  changes in chromatin organization. The promoters of genes that change  position in the LMN-Y59C mutant, are enriched for E2F (EFL-1/-2) binding  sites, consistent with previous studies implicating the Rb-E2F  interaction with lamin A in muscle dysfunction. Gene expression changes  provoked by LMN-Y59C are also largely reversed by cec-4 deletion. In  summary, the ablation of a perinuclear H3K9me-anchor can counteract the  dominant muscle-specific defects provoked by a laminopathic mutation,  implicating peripheral chromatin organization in the control of muscle  integrity.

overall_design: Total RNA-seq in synchronized L1 larval stage of Caenorhabditis elegans with the genotypes:  wild-type (samples: lmn_WT_a, lmn_WT_b) , cec-4 mutant (samples: cec4_a, cec4_b), mutant lamin (samples: lmn_Y59C_a, lmn_Y59C_b) and lamin mutant with cec-4 mutant (samples: lmn_Y59C_cec4_a, lmn_Y59C_cec4_b). 50 bp single-end sequencing was done on an Illumina HiSeq 2500.

first: Jennifer

last: Harr

first: Christoph

last: Schmid

first: Celia

last: Muñoz-Jiménez

first: Raquel

last: Romero-Bueno

first: Véronique

last: Kalck

first: Adriana

last: Gonzalez-Sandoval

first: Michael

middle: H

last: Hauer

first: Jan

last: Padeken

first: Peter

last: Askjaer

first: Anna

last: Mattout


title: Loss of a heterochromatin anchor rescues altered genome organization and EDMD muscle defects triggered by a laminopathy mutation


title: Whole transcriptome data of human liver organoids cultured in Matrigel and polyisocyanopeptides-based hydrogel

status: Public on Dec 23 2020

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

institute: Utrecht University

summary: End-stage liver diseases are an increasing health burden and liver transplantations are currently the only curative treatment option. Due to a lack of donor livers, alternative treatments are urgently needed. Human liver organoids are very promising for regenerative medicine, however, organoids are currently cultured in Matrigel, which is extracted from the extracellular matrix of the Engelbreth-Holm-Swarm mouse sarcoma. Matrigel is poorly defined, suffers from high batch-to-batch variability and is of murine origin, which limits clinical application of organoids. Here, a novel hydrogel based on polyisocyanopeptides (PIC) and laminin-111 is described for human liver organoid culture. PIC is a synthetic hydrogel with thermodynamic properties, making it easy to handle and very attractive for clinical applications. Organoids in an optimized PIC hydrogel proliferate at rates comparable to Matrigel; proliferation rates are stiffness-dependent, with lower stiffnesses being optimal for organoid proliferation. Moreover, organoids can be efficiently differentiated towards hepatocyte-like cells with key liver functions. This proliferation and differentiation potential can be maintained over at least 16 passages. Our results indicate that PIC is a promising material for human liver organoid culture and has the potential to be used in a variety of clinical applications including cell therapy and tissue engineering.

overall_design: Whole transcriptome data of human liver organoids cultured in Matrigel or a novel hybrid hydrogel based on polyisocyanopeptides (PIC) and laminin-111. Hydrogel stiffness varied by using PIC different molecular weights, namely 1 kDa PIC (1k PIC) and 5 kDa PIC (5k PIC). The proliferative capacity of organoids in hydrogel was tested by culturing in organoid expansion medium (EM). By culturing liver organoids in differentiation medium (DM) these organoids are capable to differentiate towards hepatocyte-like cells. RNA Seq data is produced on Illumina NextSeq500 using a single-end 75 bp configuration.

first: Shicheng

last: Ye

first: Jochem

last: Boeter

first: Marko

last: Mihajlovic

first: Monique

middle: E

last: van Wolferen

first: Loes

middle: A

last: Oosterhoff

first: Ary

last: Marsee

first: Massimiliano

last: Caiazzo

first: Luc

last: van der Laan

first: Louis

last: Penning

first: Tina

last: Vermonden

first: Bart

last: Spee

first: Kerstin

last: Schneeberger


title: DamID: Loss of a heterochromatin anchor rescues altered genome organization and EDMD muscle defects triggered by a laminopathy mutation

city: Seville

address: UPO Carretera de Utrera km 1

institute: Centro Andaluz de Biología del Desarrollo

summary: Point mutations in nuclear structural protein laminA produce rare and generally tissue-specific diseases called laminopathies. The introduction of a human Emery Dreifuss Muscular Dystrophy (EDMD)-inducing mutation (laminA-Y45C) into C. elegans lamin (LMN-Y59C), recapitulates many EDMD phenotypes, and results in hyper-sequestration of heterochromatic arrays at the nuclear periphery. Using muscle-specific Emerin Dam-ID we show that the LMN-Y59C mutation also leads to misorganization of endogenous chromatin. We find increased perinuclear anchoring primarily along chromosome arms, and enhanced release of chromosomal cores. Coincidentally, Y59C worms have reduced locomotion and compromised sarcomere integrity. By coupling this mutation with deletion of the perinuclear chromodomain protein CEC-4, which tethers H3K9-methylated chromatin, we rescue the EDMD-like physiology and ultrastructural defects in sarcomeres. It further counteracts the altered spatial organization of chromosomal sequences, particularly along chromosomal arms.  The data in this submission refer to the identification of chromatin enriched at the nuclear periphery (as measured by interaction with Dam::EMR-1) in muscle cells of L3/L4 control animals or cec-4 mutants expressing either GFP::LMN-1 (wild type lamin) or GFP::LMN-1(Y59C).

overall_design: Comparison of Dam::EMR-1 DNA association in wild type and cec-4(ok3124) mutants expressing either GFP::LMN-1 or GFP::LMN-1(Y59C). Strains expressing a nuclear GFP::Dam fusion were used to normalise for changes in chromatin accessibility. Using a myo-3p::FLP driver to induce genome recombination (Muñoz-Jiménez et al, PMID: 28646043), the Dam fusion proteins were expressed uniquely in intestine. Three biological replicas were prepared: all strains were grown in parallel in each replica.

first: Celia

last: Muñoz-Jiménez

first: Raquel

last: Romero-Bueno


title: Stronger induction of trained immunity by mucosal BCG or MTBVAC vaccination

status: Public on Jan 27 2021

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

summary: Vaccination against tuberculosis by intradermal Bacillus Calmette-Guérin (BCG) injection saves many lives, supposedly by inducing adaptive immune memory in lymphocytes. Epidemiologically, BCG vaccination is also associated with reduced childhood mortality unrelated to TB, which is attributed to innate immune memory, also termed trained immunity. We recently demonstrated improved protection against tuberculosis infection in highly susceptible rhesus macaques by mucosal BCG vaccination, correlating with a unique local but no peripheral immune profile. Here, we investigated local and peripheral innate immune function after intradermal versus mucosal vaccination with M. bovis BCG or the live attenuated, M. tuberculosis-derived candidate, MTBVAC. The results demonstrate an augmented frequency of trained immunity in monocytes after respiratory mucosal administration of live attenuated mycobacterial vaccines compared to intradermal immunization, with MTBVAC being equally potent as BCG. These results provide further support to strategies for improving TB vaccination and, more broadly, modulating innate immunity via mucosal surfaces.

overall_design: ChIP-seq using primate cells pre-treatment or treated with BCG

first: Michel

middle: P

last: Vierboom

first: Jorge

last: Domínguez-Andrés

first: Maarten

last: van der Sande

last: Verreck


title: RBPJ and H3K27ac chromatin IP with sequencing of CLL cells with hyperactivated Notch1 compared to control CLL cells [ChIP-seq]

status: Public on Dec 19 2020

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: NOTCH1 gain-of-function mutations are recurrent in B cell chronic lymphocytic leukemia (B-CLL), where they are associated with accelerated disease progression and refractoriness to chemotherapy. The specific role of NOTCH1 in the development and progression of this malignancy is unclear. Herein we assess the impact of loss of Notch signaling and pathway hyperactivation in an in vivo mouse model of CLL (IgH.TEm) that faithfully recapitulates many features of the human pathology. Ablation of canonical Notch signaling using conditional gene inactivation of RBP-J in immature hematopoietic or B cell progenitors delayed CLL induction and reduced incidence of mice developing disease.  In contrast, forced expression of a dominant active form of Notch resulted in more animals developing CLL with early disease onset. Comparative analysis of gene expression and epigenetic features of Notch gain-of-function and control CLL cells revealed direct and indirect regulation of cell cycle-associated genes, which led to increased proliferation of Notch gain-of-function CLL cells in vivo. These results demonstrate that Notch signaling facilitates disease initiation and promotes CLL cell proliferation and disease progression.

overall_design: RBPJ and H3K27ac ChIP-seq comparisons of sorted CLL spenocytes (CD19+B220-) derived from IgH.TEμ;RNIC del/+ mb1-Cre and  IgH.TEμ;RNIC lox/+ mice

first: Delphine

last: Tardivon

last: Zangger

first: Freddy

last: Radtke


title: Transcriptional expression data from vaccinia/HIV-1 vaccine immunized healthy subjects [in vivo]

city: Beijing

first: Yiming

last: Shao

state: Beijing

address: No. 155 Changbai Road, Changping District

department: National Center for AIDS/STD Control and Prevention

institute: Chinese Center for Disease Control and Prevention

summary: In a phase 2 trial, participants received 3 DNA/HIV-1 primes and a recombinant TV (rTV)/HIV-1 boost at 8 weeks (8-wk group) or 24 weeks (24-wk group) post-final prime. We investigated the vaccinia-specific immunological and overall transcriptomic responses to the rTV/HIV-1 boost.

overall_design:
All participants in the supplemental study received three DNA/HIV-1 primes at Weeks 0, 4, and 8, followed by a single subcutaneous dose of rTV/HIV-1 (Beijing Biological Preparations Institute Co., Ltd.). Seven of the 16 participants received the rTV/HIV-1 boost 8 weeks after the last DNA prime (8-week group), whereas the other 9 participants received the rTV/HIV-1 boost 24 weeks after the last DNA prime (24-week group). Blood was drawn from each volunteer into EDTA-2K Vacutainer tubes (BD Biosciences) on the day of the rTV/HIV-1 boost (Day 0, pre-vaccination and 4 h post-vaccination) and on Days 1, 3, 7, 9, 14, 28, 90, 180, and 360 thereafter.

DNA/HIV-1 prime = HIV-1 vaccine delivered in a DNA plasmid vector
rTV/HIV-1 = HIV-1 vaccine delivered in a Vaccinia virus vector

first: Jue

last: Hou